heatmapPlot {rrvgo} | R Documentation

## heatmapPlot Plot similarity matrix as a heatmap

### Description

heatmapPlot Plot similarity matrix as a heatmap

### Usage

    heatmapPlot(
      simMatrix,
      reducedTerms = NULL,
      annotateParent = TRUE,
      annotationLabel = "parentTerm",
      ...
    )

### Arguments

`simMatrix` | a (square) similarity matrix.
`reducedTerms` | a data.frame with the reduced terms from reduceSimMatrix()
`annotateParent` | whether to add annotation of the parent
`annotationLabel` | display "parent" ids or "parentTerm" string
`...` | other parameters sent to pheatmap::pheatmap()

### Details

Matrix with similarity scores between terms is represented as a heatmap.

### Value

Invisibly a pheatmap object that is a list with components

### Examples

    go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo"))
    simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel")
    scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID)
    reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db")
    heatmapPlot(simMatrix, reducedTerms, annotateParent=TRUE, annotationLabel="parentTerm", fontsize=6)

[Package rrvgo version 1.6.0 Index]